/SmartRoot_pipeline

Primary LanguageR

SmartRoot pipeline

  • Author: Beatriz Moreno
  • Institute: INRA

This pipeline has been designed to visualize maize lateral root length data exported with the SmartRoot ImageJ plugin.

1.Rstructuration of single root system SmartRoot files

Script location: SmartRoot_pipeline/src/SmartRoot_pipeline/1.Rstructuration/SRfiles_to_Rstructured_onePlant.R

In a first step, basic features are computed for individual roots of single root system image series, such as their root ages or daily root elongation rates.

Input files are SmartRoot CSV datasets Global Root Data, providing information about individual roots, and Root Nodes, providing information about individual nodes; both located under the data/SR_files directory. The information of individual root nodes is used to compute a basal root diameter as the median diameter of the 3 most basal nodes, and an apical root diameter for which the 3 most distant nodes are used. The date and time associated to each image acquisition must be provided in a separate CSV file, located under the data/Auxiliary_files directory.

A main output file containing complete information about individual root growth and root diameters is generated at the end of the Rstructuration script and saved under the data/Rstructured_files directory. In parallel, a short summary CSV file providing key root system properties for each image acquisition is generated and saved into data/Summary_files.

2.RPlots

Script location: SmartRoot_pipeline/src/SmartRoot_pipeline/2.Rplots/Rplots.R

The above mentioned script allows to generate interesting graphics about root growth and/or morphology in a customisable way, and export them into PDF files. Here is the list of currently available graphical representations:

  • Individual root length as function of the date of acquisition, grouped by distance from the seed into 5 cm primary root sections
  • Individual root relative elongation rate (RER) as function of root age, grouped by distance from the seed into 5 cm primary root sections
  • Individual root relative elongation rate (RER) at logaritmic scale as function of root age, grouped by distance from the seed into 5 cm primary root sections
  • Individual root elongation rate (ER) as function of root age, grouped by distance from the seed into 5 cm primary root sections
  • Individual root length as function of seed distance at the last date of acquisition
  • An histogram of root diameter to see differences in the distribution of apical relative to basal root diameters
  • Individual apical root diameter and ER as function of root length, in groups of N roots (N to be specified by the user)
  • Individual apical root diameter and ER as function of root age, in groups of N roots (N to be specified by the user)